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Chen X, Zhong S, Hou Y, Cao R, Wang W, Li D, Dai Q, Kim D, Xi P. Superresolution structured illumination microscopy reconstruction algorithms: a review. LIGHT, SCIENCE & APPLICATIONS 2023; 12:172. [PMID: 37433801 DOI: 10.1038/s41377-023-01204-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 05/24/2023] [Accepted: 06/05/2023] [Indexed: 07/13/2023]
Abstract
Structured illumination microscopy (SIM) has become the standard for next-generation wide-field microscopy, offering ultrahigh imaging speed, superresolution, a large field-of-view, and long-term imaging. Over the past decade, SIM hardware and software have flourished, leading to successful applications in various biological questions. However, unlocking the full potential of SIM system hardware requires the development of advanced reconstruction algorithms. Here, we introduce the basic theory of two SIM algorithms, namely, optical sectioning SIM (OS-SIM) and superresolution SIM (SR-SIM), and summarize their implementation modalities. We then provide a brief overview of existing OS-SIM processing algorithms and review the development of SR-SIM reconstruction algorithms, focusing primarily on 2D-SIM, 3D-SIM, and blind-SIM. To showcase the state-of-the-art development of SIM systems and assist users in selecting a commercial SIM system for a specific application, we compare the features of representative off-the-shelf SIM systems. Finally, we provide perspectives on the potential future developments of SIM.
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Affiliation(s)
- Xin Chen
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, 100871, China
- National Biomedical Imaging Center, Peking University, Beijing, 100871, China
| | - Suyi Zhong
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, 100871, China
- National Biomedical Imaging Center, Peking University, Beijing, 100871, China
| | - Yiwei Hou
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, 100871, China
- National Biomedical Imaging Center, Peking University, Beijing, 100871, China
| | - Ruijie Cao
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, 100871, China
- National Biomedical Imaging Center, Peking University, Beijing, 100871, China
| | - Wenyi Wang
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, 100871, China
- National Biomedical Imaging Center, Peking University, Beijing, 100871, China
| | - Dong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
- Beijing Key Laboratory of Multidimension & Multiscale Computational Photography, Tsinghua University, Beijing, China
- Beijing Laboratory of Brain and Cognitive Intelligence, Beijing Municipal Education Commission, Beijing, China
| | - Donghyun Kim
- School of Electrical and Electronic Engineering, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, Korea
| | - Peng Xi
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, 100871, China.
- National Biomedical Imaging Center, Peking University, Beijing, 100871, China.
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Recent Progress in the Correlative Structured Illumination Microscopy. CHEMOSENSORS 2021. [DOI: 10.3390/chemosensors9120364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The super-resolution imaging technique of structured illumination microscopy (SIM) enables the mixing of high-frequency information into the optical transmission domain via light-source modulation, thus breaking the optical diffraction limit. Correlative SIM, which combines other techniques with SIM, offers more versatility or higher imaging resolution than traditional SIM. In this review, we first briefly introduce the imaging mechanism and development trends of conventional SIM. Then, the principles and recent developments of correlative SIM techniques are reviewed. Finally, the future development directions of SIM and its correlative microscopies are presented.
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A method for the reconstruction of multifocal structured illumination microscopy data with high efficiency. Sci Rep 2019; 9:13378. [PMID: 31527605 PMCID: PMC6746813 DOI: 10.1038/s41598-019-49762-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 08/30/2019] [Indexed: 11/08/2022] Open
Abstract
We present and demonstrate an efficient method for the reconstruction of profiles acquired by multifocal structured illumination microscopy (MSIM) utilizing few raw images. Firstly, we propose a method to produce nine raw multifocal images with enhanced modulation depth to accomplish the uniform illumination of the sample. Then, combing with the parameter of the arrays, we perform the standard construct reconstruction procedure of structured illumination microscopy (SIM) row by row and column by column. Finally, we combine these restored images together to obtain the final image with enhanced resolution and good contrast. Based on theoretical analysis and numerical simulations, this method shows great potential in the field of the image reconstruction of MSIM data.
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Xue Y, So PTC. Three-dimensional super-resolution high-throughput imaging by structured illumination STED microscopy. OPTICS EXPRESS 2018; 26:20920-20928. [PMID: 30119399 DOI: 10.1364/oe.26.020920] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 07/10/2018] [Indexed: 06/08/2023]
Abstract
Stimulated emission depletion (STED) microscopy is able to image fluorescence labeled samples with nanometer scale resolution. STED microscopy is typically a point-scanning method, limited by the high intensity requirement of the depletion beam. With the development of high peak power lasers, two dimensional parallel STED microscopy has been developed. Here, we develop the theoretical basis for extending STED microscopy to three dimensional imaging in parallel. This method uses structured illumination (SI) to generates a three dimensional depletion pattern. Compared to the two dimensional parallel STED microscopy, the 3D SI-STED microscopy generates intensity modulation along the light propagation direction without requiring higher laser power. This method not only achieves axial super-resolution of STED microscopy but also greatly reduces photobleaching and photodamage for 3D volumetric imaging.
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Abstract
This review describes the growing partnership between super-resolution imaging and plasmonics, by describing the various ways in which the two topics mutually benefit one another to enhance our understanding of the nanoscale world. First, localization-based super-resolution imaging strategies, where molecules are modulated between emissive and nonemissive states and their emission localized, are applied to plasmonic nanoparticle substrates, revealing the hidden shape of the nanoparticles while also mapping local electromagnetic field enhancements and reactivity patterns on their surface. However, these results must be interpreted carefully due to localization errors induced by the interaction between metallic substrates and single fluorophores. Second, plasmonic nanoparticles are explored as image contrast agents for both superlocalization and super-resolution imaging, offering benefits such as high photostability, large signal-to-noise, and distance-dependent spectral features but presenting challenges for localizing individual nanoparticles within a diffraction-limited spot. Finally, the use of plasmon-tailored excitation fields to achieve subdiffraction-limited spatial resolution is discussed, using localized surface plasmons and surface plasmon polaritons to create confined excitation volumes or image magnification to enhance spatial resolution.
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Affiliation(s)
- Katherine A Willets
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - Andrew J Wilson
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - Vignesh Sundaresan
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - Padmanabh B Joshi
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
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Neupane B, Jin T, Mellor LF, Loboa EG, Ligler FS, Wang G. Continuous-Wave Stimulated Emission Depletion Microscope for Imaging Actin Cytoskeleton in Fixed and Live Cells. SENSORS 2015; 15:24178-90. [PMID: 26393614 PMCID: PMC4610488 DOI: 10.3390/s150924178] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 09/12/2015] [Accepted: 09/16/2015] [Indexed: 11/16/2022]
Abstract
Stimulated emission depletion (STED) microscopy provides a new opportunity to study fine sub-cellular structures and highly dynamic cellular processes, which are challenging to observe using conventional optical microscopy. Using actin as an example, we explored the feasibility of using a continuous wave (CW)-STED microscope to study the fine structure and dynamics in fixed and live cells. Actin plays an important role in cellular processes, whose functioning involves dynamic formation and reorganization of fine structures of actin filaments. Frequently used confocal fluorescence and STED microscopy dyes were employed to image fixed PC-12 cells (dyed with phalloidin- fluorescein isothiocyante) and live rat chondrosarcoma cells (RCS) transfected with actin-green fluorescent protein (GFP). Compared to conventional confocal fluorescence microscopy, CW-STED microscopy shows improved spatial resolution in both fixed and live cells. We were able to monitor cell morphology changes continuously; however, the number of repetitive analyses were limited primarily by the dyes used in these experiments and could be improved with the use of dyes less susceptible to photobleaching. In conclusion, CW-STED may disclose new information for biological systems with a proper characteristic length scale. The challenges of using CW-STED microscopy to study cell structures are discussed.
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Affiliation(s)
- Bhanu Neupane
- Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Raleigh, NC 27695, USA.
| | - Tao Jin
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA.
| | - Liliana F Mellor
- Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Raleigh, NC 27695, USA.
| | - Elizabeth G Loboa
- Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Raleigh, NC 27695, USA.
| | - Frances S Ligler
- Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Raleigh, NC 27695, USA.
| | - Gufeng Wang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA.
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Abstract
Light microscopy plays a key role in biological studies and medical diagnosis. The spatial resolution of conventional optical microscopes is limited to approximately half the wavelength of the illumination light as a result of the diffraction limit. Several approaches-including confocal microscopy, stimulated emission depletion microscopy, stochastic optical reconstruction microscopy, photoactivated localization microscopy, and structured illumination microscopy-have been established to achieve super-resolution imaging. However, none of these methods is suitable for the super-resolution ophthalmoscopy of retinal structures because of laser safety issues and inevitable eye movements. We recently experimentally validated virtually structured detection (VSD) as an alternative strategy to extend the diffraction limit. Without the complexity of structured illumination, VSD provides an easy, low-cost, and phase artifact-free strategy to achieve super-resolution in scanning laser microscopy. In this article we summarize the basic principles of the VSD method, review our demonstrated single-point and line-scan super-resolution systems, and discuss both technical challenges and the potential of VSD-based instrumentation for super-resolution ophthalmoscopy of the retina.
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Affiliation(s)
- Yanan Zhi
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL
| | - Benquan Wang
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL
| | - Xincheng Yao
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL
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Plasmon based super resolution imaging for single molecular detection: Breaking the diffraction limit. Biomed Eng Lett 2014. [DOI: 10.1007/s13534-014-0154-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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Sonnefraud Y, Sinclair HG, Sivan Y, Foreman MR, Dunsby CW, Neil MAA, French PM, Maier SA. Experimental proof of concept of nanoparticle-assisted STED. NANO LETTERS 2014; 14:4449-4453. [PMID: 25053232 DOI: 10.1021/nl5014103] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We imaged core-shell nanoparticles, consisting of a dye-doped silica core covered with a layer of gold, with a stimulated emission depletion, fluorescence lifetime imaging (STED-FLIM) microscope. Because of the field enhancement provided by the localized surface plasmon resonance of the gold shell, we demonstrate a reduction of the STED depletion power required to obtain resolution improvement by a factor of 4. This validates the concept of nanoparticle-assisted STED (NP-STED), where hybrid dye-plasmonic nanoparticles are used as labels for STED in order to decrease the depletion powers required for subwavelength imaging.
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Affiliation(s)
- Yannick Sonnefraud
- Institut Néel, CNRS UPR 2940 , 25 rue des Martyrs BP 166, 38042 Grenoble Cedex 9, France
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Neupane B, Ligler FS, Wang G. Review of recent developments in stimulated emission depletion microscopy: applications on cell imaging. JOURNAL OF BIOMEDICAL OPTICS 2014; 19:080901. [PMID: 25121478 DOI: 10.1117/1.jbo.19.8.080901] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 07/21/2014] [Indexed: 06/03/2023]
Abstract
Stimulated emission depletion (STED) microscopy is one type of far-field optical technique demonstrated to provide subdiffraction resolution. STED microscopy utilizes a donut-shaped depletion beam to limit the probe volume to be much smaller than a diffraction-limited spot. Resolutions as small as a few tens of nanometers laterally are reported for cell analysis. The different versions of STED microscopes are described and contrasted in terms of their applicability for biological imaging. Finally, we suggest likely avenues for improving the performance and increasing the utility of STED microscopy.
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Affiliation(s)
- Bhanu Neupane
- University of North Carolina at Chapel Hill and North Carolina State University, Department of Biomedical Engineering, Raleigh, North Carolina 27599-7115, United States
| | - Frances S Ligler
- University of North Carolina at Chapel Hill and North Carolina State University, Department of Biomedical Engineering, Raleigh, North Carolina 27599-7115, United States
| | - Gufeng Wang
- North Carolina State University, Department of Chemistry, Raleigh, North Carolina 27695-8204, United States
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Zhao M, Zhang H, Li Y, Ashok A, Liang R, Zhou W, Peng L. Cellular imaging of deep organ using two-photon Bessel light-sheet nonlinear structured illumination microscopy. BIOMEDICAL OPTICS EXPRESS 2014; 5:1296-308. [PMID: 24876996 PMCID: PMC4026892 DOI: 10.1364/boe.5.001296] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 03/24/2014] [Accepted: 03/24/2014] [Indexed: 05/18/2023]
Abstract
In vivo fluorescent cellular imaging of deep internal organs is highly challenging, because the excitation needs to penetrate through strong scattering tissue and the emission signal is degraded significantly by photon diffusion induced by tissue-scattering. We report that by combining two-photon Bessel light-sheet microscopy with nonlinear structured illumination microscopy (SIM), live samples up to 600 microns wide can be imaged by light-sheet microscopy with 500 microns penetration depth, and diffused background in deep tissue light-sheet imaging can be reduced to obtain clear images at cellular resolution in depth beyond 200 microns. We demonstrate in vivo two-color imaging of pronephric glomeruli and vasculature of zebrafish kidney, whose cellular structures located at the center of the fish body are revealed in high clarity by two-color two-photon Bessel light-sheet SIM.
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Affiliation(s)
- Ming Zhao
- College of Optical Sciences, the University of Arizona, 1630 East University Blvd., Tucson, AZ 85721, USA
| | - Han Zhang
- College of Optical Sciences, the University of Arizona, 1630 East University Blvd., Tucson, AZ 85721, USA
| | - Yu Li
- College of Optical Sciences, the University of Arizona, 1630 East University Blvd., Tucson, AZ 85721, USA
| | - Amit Ashok
- College of Optical Sciences, the University of Arizona, 1630 East University Blvd., Tucson, AZ 85721, USA
| | - Rongguang Liang
- College of Optical Sciences, the University of Arizona, 1630 East University Blvd., Tucson, AZ 85721, USA
| | - Weibin Zhou
- Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, Michigan, MI 48109, USA
| | - Leilei Peng
- College of Optical Sciences, the University of Arizona, 1630 East University Blvd., Tucson, AZ 85721, USA
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12
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Dan D, Yao B, Lei M. Structured illumination microscopy for super-resolution and optical sectioning. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s11434-014-0181-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Neupane B, Chen F, Sun W, Chiu DT, Wang G. Tuning donut profile for spatial resolution in stimulated emission depletion microscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2013; 84:043701. [PMID: 23635197 PMCID: PMC3637329 DOI: 10.1063/1.4799665] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 03/20/2013] [Indexed: 05/29/2023]
Abstract
In stimulated emission depletion (STED)-based or up-conversion depletion-based super-resolution optical microscopy, the donut-shaped depletion beam profile is of critical importance to its resolution. In this study, we investigate the transformation of the donut-shaped depletion beam focused by a high numerical aperture (NA) microscope objective, and model STED point spread function (PSF) as a function of donut beam profile. We show experimentally that the intensity profile of the dark kernel of the donut can be approximated as a parabolic function, whose slope is determined by the donut beam size before the objective back aperture, or the effective NA. Based on this, we derive the mathematical expression for continuous wave (CW) STED PSF as a function of focal plane donut and excitation beam profiles, as well as dye properties. We find that the effective NA and the residual intensity at the center are critical factors for STED imaging quality and the resolution. The effective NA is critical for STED resolution in that it not only determines the donut shape but also the area the depletion laser power is dispersed. An improperly expanded depletion beam will have negligible improvement in resolution. The polarization of the depletion beam also plays an important role as it affects the residual intensity in the center of the donut. Finally, we construct a CW STED microscope operating at 488 nm excitation and 592 nm depletion with a resolution of 70 nm. Our study provides detailed insight to the property of donut beam, and parameters that are important for the optimal performance of STED microscopes. This paper will provide a useful guide for the construction and future development of STED microscopes.
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Affiliation(s)
- Bhanu Neupane
- Chemistry Department, North Carolina State University, Raleigh, North Carolina 27695, USA
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Abstract
Plasmonics and near-field optical nanoscopy both deal with expanding optics into the subwavelength regime. However, these two fields have so far followed parallel paths of development and only recently have researchers started to explore combinations of their concepts with potential synergy. In this Perspective, we provide an up-to-date summary of the successful combinations reported and give insight into some new possibilities.
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Affiliation(s)
- Francisco Balzarotti
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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